Commits for mspeir

v293_preview2 to v293_base (2013-12-02 to 2013-12-09) v293

• Organized mirror page by geographical location, plus fixed some other links, refs #12175
  • src/hg/htdocs/mirror.html - lines changed 147, context: html, text, full: html, text
• Changing some links on anoCar2 track description pages
  • src/hg/makeDb/trackDb/blastHg18KG.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lizard/anoCar2/cons7way.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lizard/anoCar2/description.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/simpleRepeat.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tRNAs.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenoRefGene.html - lines changed 1, context: html, text, full: html, text
• Changing release tags for mm10 MGI QTL track, refs #7040
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 1, context: html, text, full: html, text
• Added a small map to each section. Alphabetized continents. Added disclaimer at top to emphasize fact that these are mirrors not maintained or supported by UCSC. Map files are included in this commit, refs #12175
  • src/hg/htdocs/images/mapAustralia.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/mapEuro.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/images/mapNAmer.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/htdocs/mirror.html - lines changed 102, context: html, text, full: html, text
• Making some small wording changes based on Code Review, refs #12247
  • src/product/README.requirements - lines changed 6, context: html, text, full: html, text
• Adding line about Apache web server under software requirements, refs #12247, #11941
  • src/product/README.requirements - lines changed 1, context: html, text, full: html, text
• Fixing some links on gibbon track description pages
  • src/hg/makeDb/trackDb/gibbon/nomLeu2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu2/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu2/gold.html - lines changed 1, context: html, text, full: html, text
• Fixing some links on turkey track description pages
  • src/hg/makeDb/trackDb/nscanGene.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/turkey/melGal1/description.html - lines changed 2, context: html, text, full: html, text
• Fixing some saiBol1 track description page links
  • src/hg/makeDb/trackDb/saiBol/saiBol1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/gold.html - lines changed 1, context: html, text, full: html, text
• Fixing some links on dog track description pages
  • src/hg/makeDb/trackDb/dog/canFam3/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam3/gold.html - lines changed 1, context: html, text, full: html, text
• Changing some links on naked mole rat track description pages
  • src/hg/makeDb/trackDb/moleRat/hetGla2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla2/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla2/gold.html - lines changed 1, context: html, text, full: html, text
• correcting links on track description pages for a number of worm species
  • src/hg/makeDb/trackDb/blastHg16KG.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/blatFr1.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/geneid.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/phastConsElements.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rnaCluster.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/twinscan.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/blastCe4SG.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/blastCe6SG.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeJap1/description.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem3/ctgPos2.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem3/description.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem3/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeRem3/gold.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb1/blastzCe1.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb1/blastzCe2.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb1/ce1Chain.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb1/chainCe2.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb3/description.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb3/gap.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb3/gold.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/cons7way.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/cons9way.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/axtNetCb1.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/blastzSelf.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/c_briggsae_pwMaf.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/chainCb1.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/netCb1.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/picTar.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/sangerGenefinder.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/wabaCbr.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/multiz5way.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/multiz6way.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce6/phastConsElements6way.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCaeJap1.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCaePb1.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCaePb2.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCaeRem2.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCaeRem3.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCb3.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCe4.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainCe6.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainPriPac1.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/chainSelf.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/est.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/htmlPages - lines changed 187, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/intronEst.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/mrna.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCaeJap1.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCaePb1.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCaePb2.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCaeRem2.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCaeRem3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCb3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCe4.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netCe6.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/netPriPac1.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/refGene.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/xenoMrna.html - lines changed 1, context: html, text, full: html, text
• Removed temp file I accidentally added
  • src/hg/makeDb/trackDb/worm/htmlPages - lines changed 187, context: html, text, full: html, text
• Changing links for both droAna assemblies
  • src/hg/makeDb/trackDb/blastDm2FB.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chainDm2.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chainDm3.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna2/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna2/gap.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna2/gold.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/mrna.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/rmsk.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/xenoMrna.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/xenoRefGene.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/netDm2.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/netDm3.html - lines changed 1, context: html, text, full: html, text
• Correcting more links on worm track description pages
  • src/hg/makeDb/trackDb/worm/caeRem3/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb3/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/cb3/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/description.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/gold.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/gold.html - lines changed 1, context: html, text, full: html, text
• Correcting even more links I missed on worm track description pages
  • src/hg/makeDb/trackDb/sibTxGraph.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeJap1/ctgPos2.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce10/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/blastzCb1.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/multiz5way.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/phastConsElements5way.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/ce4/transcriptome.html - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/nucleosome.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/nucleosomeAdjustedCoverage.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/nucleosomeControlCoverage.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/nucleosomeDensity.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/nucleosomeStringency.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/refGene.html - lines changed 1, context: html, text, full: html, text
• Fixing more links on droAna track description pages
  • src/hg/makeDb/trackDb/chainDm3.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/chainDm2.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/mrna.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/refGene.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/xenoMrna.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/xenoRefGene.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/netDm3.html - lines changed 2, context: html, text, full: html, text
• Adding pubmed links to references for UCSF Brain Methylation track, refs #2540
  • src/hg/makeDb/trackDb/human/ucsfBrainMethyl.html - lines changed 52, context: html, text, full: html, text
• Correcting links on zebrafish track description pages
  • src/hg/makeDb/trackDb/zebrafish/danRer7/cons8way.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer7/danRer7multipleChainNet.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer7/description.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/danRer7/gold.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/mgcFullMrna.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/zebrafish/mgcGenes.html - lines changed 1, context: html, text, full: html, text
• Correcting links on squirt track description pages
  • src/hg/makeDb/trackDb/squirt/all_est.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/all_mrna.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/ci2/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/intronEst.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/refGene.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/rmsk.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/xenoMrna.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirt/xenoRefGene.html - lines changed 2, context: html, text, full: html, text
• Changing links on apiMel track description pages
  • src/hg/makeDb/trackDb/apis/all_est.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/all_mrna.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/chainDm1.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/intronEst.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/rmsk.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/xenoMrna.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/blastDm1FB.html - lines changed 2, context: html, text, full: html, text
• Correcting links on cat (felCat3) track description pages
  • src/hg/makeDb/trackDb/cat/felCat3/description.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat3/multiz4way.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat3/phastConsElements4way.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cat/felCat3/xenoRefGene.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/microsat.html - lines changed 1, context: html, text, full: html, text
• Correcting links on horse (equCab1) track description pages
  • src/hg/makeDb/trackDb/horse/equCab1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/sgpGene.html - lines changed 1, context: html, text, full: html, text
• Changing some links on various chimp (panTro1) track description pages
  • src/hg/makeDb/trackDb/chimp/bacEndPairs.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/axtNetHg16.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/ctgPos.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/gold.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/humanDels.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro1/xenoRefGeneNoHs.html - lines changed 1, context: html, text, full: html, text
• Changing some links on various track description pages for speTri2, sorAra1, hetGla1, nomLeu1, and bosTau7
  • src/hg/makeDb/trackDb/cow/bosTau7/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/gibbon/nomLeu1/description.html - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra1/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra1/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra1/gold.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/description.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/gap.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/gold.html - lines changed 1, context: html, text, full: html, text
• Removed stanza for non-existent snpArray track, refs #12227
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 4, context: html, text, full: html, text
• Correcting links on marmoset (calJac1) track description pages
  • src/hg/makeDb/trackDb/marmoset/calJac1/description.html - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/multiz9way.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/nscanGene.html - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac1/phastConsElements9way.html - lines changed 5, context: html, text, full: html, text